Mapsembler2

[page edited on Octobber, 31th, 2014]

Mapsembler2 description and possible usages:

Mapsembler2 is a targeted assembly software. It takes as input any number of NGS raw read set(s) (fasta or fastq, gzipped or not) and a set of input sequences (starters). For each starter, Mapsembler2 outputs its sequence neighborhood as a linear sequence or as a graph, depending on the user choice. Mapsembler2 may be used for (not limited to): · Validate an assembled sequence (input as starter), e.g. from a de Bruijn graph assembly where read-coherence was not enforced. Checks if a known enzyme is present in a metagenomic NGS read set. · Enrich unmappable reads by extending them, possibly making them mappable · Checks what happens at the extremities of a contig · Check the presence / absence and quantify RNA seq splicing events. Check the presence/absence of SNPs or structural variants, …

What’s new in Mapsembler2?

Two main novelties are implemented in mapsembler2:

The Minia data structure is now used for indexing reads. For the price of using a few Gigabytes RAM, Mapsembler2 is much faster as it reads the read files only once.

The starters are only extended. Mapsembler does not search for all (possibly numerous) sub-starters.